Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	130,854	(T)5→1	9.9%	intergenic (‑94/+272)	sarS ← / ← yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 130853	55 (0.880)	6 (0.100)	6/256	NT	9.9%	intergenic (‑93/+276)	sarS/yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA
	?	USA300TCH1516_ALE	130858 =	55 (0.880)					intergenic (‑98/+271)	sarS/yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA

TCAATGATTATAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGGTGTTATTTGTATATAAAG  >  USA300TCH1516_ALE/130714‑130992                                                                                                                                            |                                                                                                                                            tCAATGATTATAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATAT                                                                                                                                             <  1:376328‑M1/140‑1 (MQ=255) tCAATGATTATAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATAT                                                                                                                                             <  1:449766‑M1/140‑1 (MQ=255)     tGATTATAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTAAAATTAAAAATAATATAATAttttt                                                                                                                                         >  2:681898/1‑140 (MQ=255)       aTTATAAAATCTCTAATTTTGTCATGGTCATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATattaaa                                                                                                                                       <  2:640533‑M1/140‑7 (MQ=255)         tataAAATCTCCAATTTTGTCATGGTTATTATATTTCATTGTATTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAATCAAAATAATACTTAATGTAAAATTAAAAATAATATGTTATattcaaat                                                                                                                                     >  2:131092‑M1/1‑132 (MQ=255)              aaTCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAAtt                                                                                                                                <  1:534454/140‑1 (MQ=255)                  tctAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTAGTAAAATTtgtg                                                                                                                            >  2:629589/1‑140 (MQ=255)                      aTTTTGTCATTGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                        <  1:184869/140‑1 (MQ=255)                      aTTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                        <  1:635295/140‑1 (MQ=255)                      aTTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                        <  2:606692/140‑1 (MQ=255)                      aTTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                        <  1:306796/140‑1 (MQ=255)                      aTTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                        <  2:214299/140‑1 (MQ=255)                           gTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAAt                                                                                                                   <  1:339080/140‑1 (MQ=255)                            tCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATACTTTACGATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATa                                                                                                                  >  1:719057/1‑140 (MQ=255)                             cacggTTATGATATTTCATTGTTTTTTCTCCTTGTATATGCACTTTATTTTAATATGATATATTATAATATGAAAAATAATCTATAATTTAAAATGAACAATTATATGATATTTTTATTAAAATTCTTATTTTTtaataa                                                                                                                 >  2:177143/4‑140 (MQ=255)                                  ttattaTATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGAc                                                                                                            <  2:92927/140‑1 (MQ=255)                                  ttattaTATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGAc                                                                                                            <  1:215272/140‑1 (MQ=255)                                      tataTTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTa                                                                                                        <  2:28237/140‑1 (MQ=255)                                      tataTTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTa                                                                                                        <  2:29601/140‑1 (MQ=255)                                        tatTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATc                                                                                                      <  1:597666/140‑1 (MQ=255)                                        tatTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATc                                                                                                      <  1:597814/140‑1 (MQ=255)                                        tatTTCATTATTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATattaaaatttgtgtttttgaataaatgacattatcaaac                                                                                                      <  2:540039‑M1/140‑40 (MQ=255)                                               ttGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACt                                                                                               <  1:260681/140‑1 (MQ=255)                                                tGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACta                                                                                              >  1:709436/1‑140 (MQ=255)                                                tGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACAAAATATAATAAGAGAAATAATCCATAATTTACAGTTAAAAATAATATGATATTTTTATTAACATTTGTGTCTTTGAATAAATGACATTATCAAACACtc                                                                                              >  1:17964/1‑139 (MQ=255)                                                 gTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATattaaaatttgtgtttttgaataaatgacattatcaaacactatattt                                                                                             >  1:75600‑M1/1‑92 (MQ=255)                                                  ttttATCTCCTTTTATATGCGCTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACtata                                                                                            <  2:25627/140‑1 (MQ=255)                                                       tctcCTTGTATATGCACTTTATTTTAATATCACATTATCTAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTaa                                                                                       >  2:54224/1‑140 (MQ=255)                                                        ctcCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTaaa                                                                                      >  1:252718/1‑140 (MQ=255)                                                           cTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGACTAAATGACATTATCAAACACTATATTTAAATaa                                                                                   >  1:260022/1‑140 (MQ=255)                                                              ttataTGCACTTTCTTTTAATATAACACAATATAATAGTAAAAATAATCCATAAGTTACAATTAAAAATAATATGATATTTTTACAACAATTTGTGTTTTTTAATAAATGACATTATCAAACACTATATTTAAATAAGaa                                                                                <  2:744800/139‑1 (MQ=255)                                                              atataTGCACTTTAGTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGaa                                                                                <  1:568976/139‑1 (MQ=255)                                                                atatGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATattaaaatttgtgtttttgaataaatgacattatcaaacactatatttaaataagaaatagtt                                                                              >  2:119955‑M1/1‑77 (MQ=255)                                                                 tatGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATa                                                                             <  2:623540/140‑1 (MQ=255)                                                                        tttATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAGTATTATATTTTTATTAAAATTTGTGTTTTTGCATAAATGACCTTATCATCCACGCTATTTAACTACGAAATACTtctct                                                                      >  1:651975/1‑139 (MQ=255)                                                                         ttATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATATATGACAGAACCAAACACTATATTTATATAGGAAATAGTTATGGa                                                                     >  1:140243/1‑140 (MQ=255)                                                                            ttttAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGatat                                                                  >  1:733444/1‑140 (MQ=255)                                                                             tttAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATAtt                                                                 <  1:762950/140‑1 (MQ=255)                                                                             tttAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATAtt                                                                 >  2:278783/1‑140 (MQ=255)                                                                              ttAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATAttt                                                                >  1:533997/1‑140 (MQ=255)                                                                                 atatAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGaa                                                             <  2:57701/140‑1 (MQ=255)                                                                                 atatAACAAAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGaa                                                             <  2:395207/140‑1 (MQ=255)                                                                                   ataACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGaaaa                                                           <  2:26138/140‑1 (MQ=255)                                                                                      acacAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATc                                                        >  1:546604/1‑140 (MQ=255)                                                                                      acacAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATc                                                        >  2:748396/1‑140 (MQ=255)                                                                                      acacAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATc                                                        >  2:400854/1‑140 (MQ=255)                                                                                             ataataataAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGTTATTTGAAAAATCGAAGAat                                                 <  2:320199/140‑1 (MQ=255)                                                                                             ataataAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAat                                                 <  2:191073/140‑1 (MQ=255)                                                                                             agaataaGAAAAATAATTCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAat                                                 <  2:168932/138‑1 (MQ=255)                                                                                               aataaGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTGTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAatat                                               <  1:68066/140‑1 (MQ=255)                                                                                                ataaGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTACAATTTGTGTTTTTGAATAAATGCCATTTGCGAACACTATATTTCAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAAtttt                                              >  1:175663/1‑140 (MQ=255)                                                                                                ataaGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATatt                                              >  1:364722/1‑140 (MQ=255)                                                                                                     aaaaaTAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATattgattg                                         >  1:179888/1‑140 (MQ=255)                                                                                                     aaaaaTAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATattgattg                                         <  1:6546/140‑1 (MQ=255)                                                                                                      aaaaTAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATAGAAGAATAttgattga                                        >  2:115671/1‑140 (MQ=255)                                                                                                          taatCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGAtatt                                    <  2:733444/140‑1 (MQ=255)                                                                                                             tCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTAAAAAATCGAAGAATATTGATTGACATtata                                 >  1:715161/1‑140 (MQ=255)                                                                                                              ccATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAg                                >  1:662748/1‑140 (MQ=255)                                                                                                                aTAATTTACAATTAAAAATAATATGATATattaaaatttgtgtttttgaataaatgacattatcaaacactatatttaaataagaaatagttatcgatatttgaaaaatcgaagaatattgattgatattatagaatatg                              <  2:354933‑M1/140‑112 (MQ=255)                                                                                                                        cAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTc                      >  1:747640/1‑140 (MQ=255)                                                                                                                           ttAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGgt                   <  2:443239/140‑1 (MQ=255)                                                                                                                           ttAAAAATAATATCAAATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGgt                   <  1:751928/140‑1 (MQ=255)                                                                                                                            tAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGgtg                  <  2:8893/140‑1 (MQ=255)                                                                                                                                    atatGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATCTTTGAAAAATCGAAGACTCTAGATCGTTATAAGAGAATATGAGTCGGTGTTATTTGt          >  1:477334/1‑140 (MQ=255)                                                                                                                                            tttttATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGGTGTTATTTGTATATAAAg  <  2:130988/140‑1 (MQ=255)                                                                                                                                            tattaaaatttgtgtttttgaataaatgacattatcaaacactatatttaaataagaaatagttatcgatatttgaaaaatcgaagaatattgattgatattatagaatatgagtcggtgttatttgtatataaagtatt  >  1:29979‑M1/1‑1 (MQ=255)                                                                                                                                            |                                                                                                                                            TCAATGATTATAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGGTGTTATTTGTATATAAAG  >  USA300TCH1516_ALE/130714‑130992

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.